seqtree 0.0.1__tar.gz
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- seqtree-0.0.1/.gitattributes +1 -0
- seqtree-0.0.1/.gitignore +12 -0
- seqtree-0.0.1/CMakeLists.txt +53 -0
- seqtree-0.0.1/LICENSE +674 -0
- seqtree-0.0.1/PKG-INFO +111 -0
- seqtree-0.0.1/README.md +82 -0
- seqtree-0.0.1/include/seqtree/seqtree.hpp +102 -0
- seqtree-0.0.1/include/seqtree/types.hpp +58 -0
- seqtree-0.0.1/pyproject.toml +44 -0
- seqtree-0.0.1/python/seqtree/__init__.py +10 -0
- seqtree-0.0.1/python/seqtree/py.typed +0 -0
- seqtree-0.0.1/src/_bindings.cpp +235 -0
- seqtree-0.0.1/src/blosum62.inc +31 -0
- seqtree-0.0.1/src/codec.cpp +37 -0
- seqtree-0.0.1/src/engine_seqtm.cpp +81 -0
- seqtree-0.0.1/src/engine_seqtrie.cpp +69 -0
- seqtree-0.0.1/src/engines.hpp +35 -0
- seqtree-0.0.1/src/index.cpp +142 -0
- seqtree-0.0.1/src/searcher.cpp +94 -0
- seqtree-0.0.1/src/substitution_matrix.cpp +35 -0
- seqtree-0.0.1/src/trie.cpp +98 -0
- seqtree-0.0.1/src/trie.hpp +43 -0
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tests/cpp/doctest.h linguist-vendored
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seqtree-0.0.1/.gitignore
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cmake_minimum_required(VERSION 3.20)
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project(seqtree LANGUAGES CXX)
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set(CMAKE_CXX_STANDARD 20)
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set(CMAKE_CXX_STANDARD_REQUIRED ON)
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set(CMAKE_POSITION_INDEPENDENT_CODE ON)
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if(NOT CMAKE_BUILD_TYPE)
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set(CMAKE_BUILD_TYPE Release)
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endif()
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set(CMAKE_CXX_FLAGS_RELEASE "-O3")
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option(SEQTREE_TESTS "Build C++ tests" OFF)
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option(SEQTREE_BENCH "Build C++ benchmarks" OFF)
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option(SEQTREE_PYTHON "Build the pybind11 module" OFF)
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find_package(Threads REQUIRED)
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add_library(seqtree_core STATIC
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src/codec.cpp
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src/substitution_matrix.cpp
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src/trie.cpp
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src/index.cpp
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src/engine_seqtm.cpp
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src/engine_seqtrie.cpp
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src/searcher.cpp
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)
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target_include_directories(seqtree_core PUBLIC include PRIVATE src)
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target_link_libraries(seqtree_core PUBLIC Threads::Threads)
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if(SEQTREE_PYTHON)
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find_package(pybind11 CONFIG REQUIRED)
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pybind11_add_module(_core src/_bindings.cpp)
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target_link_libraries(_core PRIVATE seqtree_core)
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install(TARGETS _core DESTINATION seqtree)
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endif()
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if(SEQTREE_TESTS)
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enable_testing()
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add_executable(seqtree_tests
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tests/cpp/test_codec.cpp
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tests/cpp/test_matrix.cpp
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tests/cpp/test_trie.cpp
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tests/cpp/test_engines.cpp
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)
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target_include_directories(seqtree_tests PRIVATE tests/cpp src)
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target_link_libraries(seqtree_tests PRIVATE seqtree_core)
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add_test(NAME seqtree_tests COMMAND seqtree_tests)
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endif()
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if(SEQTREE_BENCH)
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add_executable(seqtree_bench bench/bench_seqtree.cpp)
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target_link_libraries(seqtree_bench PRIVATE seqtree_core)
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endif()
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